Difference between revisions of "SLab:Run Processing"
From CCGB
(→Illumina) |
(→454) |
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| Line 1: | Line 1: | ||
= 454 = | = 454 = | ||
| + | |||
; systems | ; systems | ||
* schuster-flx1 | * schuster-flx1 | ||
| Line 5: | Line 6: | ||
* schuster-flx3 | * schuster-flx3 | ||
* schuster-flx4 | * schuster-flx4 | ||
| + | |||
| + | == on-rig processing == | ||
| + | * run directories are stored in /data | ||
| + | ** /data/YYYY_MM_DD/R_YYYY_MM_DD_HH_MM_SS_RIGNAME_OPERATOR_RUNNAME | ||
| + | * when a run finishes processing, it calls the /usr/local/rig/bin/postAnalysisScript.sh script | ||
| + | ** rsync's run directory to s2:/zfs/md1k-4/data/sequencing/temp/454 | ||
| + | ** ssh's to c1.persephone to submit job | ||
| + | *** depending on run | ||
| + | **** calls c1.persephone:/usr/local/bin/submit-signalProcessing.sh | ||
| + | **** calls c1.persephone:/usr/local/bin/submit-fullProcessing.sh | ||
| + | ** status email is sent to 454pipeline@bx.psu.edu | ||
| + | ** our postAnalysisScript.sh is kept in /home/adminrig/postAnalysisScript directory on each rig | ||
| + | *** revision controlled using rcs | ||
| + | **** % co -l postAnalysisScript.sh | ||
| + | **** % vi postAnalysisScript.sh | ||
| + | **** % ci -u postAnalysisScript.sh | ||
| + | *** Makefile in this directory installs our version into /usr/local/rig/bin | ||
| + | **** % make install | ||
| + | |||
| + | == signal processing == | ||
| + | * signal processing for runs is performed on the persephone cluster | ||
| + | * depending on run | ||
| + | ** uses qsub to submit job using c1.persephone:/usr/local/bin/signalProcessing.qsub | ||
| + | ** uses qsub to submit job using c1.persephone:/usr/local/bin/fullProcessing.qsub | ||
| + | * status email is sent to 454pipeline@bx.psu.edu | ||
= Illumina = | = Illumina = | ||
; systems | ; systems | ||
* illumina-ga | * illumina-ga | ||
Revision as of 11:01, 12 March 2010
454
- systems
- schuster-flx1
- schuster-flx2
- schuster-flx3
- schuster-flx4
on-rig processing
- run directories are stored in /data
- /data/YYYY_MM_DD/R_YYYY_MM_DD_HH_MM_SS_RIGNAME_OPERATOR_RUNNAME
- when a run finishes processing, it calls the /usr/local/rig/bin/postAnalysisScript.sh script
- rsync's run directory to s2:/zfs/md1k-4/data/sequencing/temp/454
- ssh's to c1.persephone to submit job
- depending on run
- calls c1.persephone:/usr/local/bin/submit-signalProcessing.sh
- calls c1.persephone:/usr/local/bin/submit-fullProcessing.sh
- depending on run
- status email is sent to 454pipeline@bx.psu.edu
- our postAnalysisScript.sh is kept in /home/adminrig/postAnalysisScript directory on each rig
- revision controlled using rcs
- % co -l postAnalysisScript.sh
- % vi postAnalysisScript.sh
- % ci -u postAnalysisScript.sh
- Makefile in this directory installs our version into /usr/local/rig/bin
- % make install
- revision controlled using rcs
signal processing
- signal processing for runs is performed on the persephone cluster
- depending on run
- uses qsub to submit job using c1.persephone:/usr/local/bin/signalProcessing.qsub
- uses qsub to submit job using c1.persephone:/usr/local/bin/fullProcessing.qsub
- status email is sent to 454pipeline@bx.psu.edu
Illumina
- systems
- illumina-ga
